7ZEQ | pdb_00007zeq

Apo crystal structure of beta-xylosidase from Thermotoga maritima

PDB DOI: https://doi.org/10.2210/pdb7ZEQ/pdb

Classification: HYDROLASE
Organism(s): Thermotoga maritima MSB8
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2022-03-31 Released: 2023-04-19
Deposition Author(s): Gloster, T.M., Foltanyi, F.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free:
0.226 (Depositor), 0.230 (DCC)
R-Value Work:
0.194 (Depositor), 0.190 (DCC)

Starting Models: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structural and further functional characterisation of a glycoside hydrolase family 3 beta-xylosidase from Thermotoga maritima

Gloster, T.M., Foltanyi, F., Hobbs, E.M., Pritchard, L.

To be published.

Macromolecule Content

Total Structure Weight: 179.69 kDa
Atom Count: 11,961
Modeled Residue Count: 1,513
Deposited Residue Count: 1,602
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Beta-xylosidase	A [auth X], B [auth Y]	801	Thermotoga maritima MSB8	Mutation(s): 0 Gene Names: Tmari_0073 EC: 3.2.1.37
UniProt
Find proteins for Q9WXT1 (Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8)) Explore Q9WXT1 Go to UniProtKB: Q9WXT1
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9WXT1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MPD Query on MPD Download Ideal Coordinates CCD File SDF format, chain C [auth X] SDF format, chain D [auth Y] MOL2 format, chain C [auth X] MOL2 format, chain D [auth Y] mmCIF format, chain C [auth X] mmCIF format, chain D [auth Y]	C [auth X], D [auth Y]	(4S)-2-METHYL-2,4-PENTANEDIOL C₆ H₁₄ O₂ SVTBMSDMJJWYQN-YFKPBYRVSA-N		Interactions Focus chain C [auth X] Focus chain D [auth Y] Interactions & Density Focus chain C [auth X] Focus chain D [auth Y]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free: 0.226 (Depositor), 0.230 (DCC)
R-Value Work: 0.194 (Depositor), 0.190 (DCC)

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 179.08	α = 90
b = 98.59	β = 90
c = 100.92	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2023-04-19

Deposition Author(s):

Funding Organization	Location	Grant Number
Other government		--

Revision History (Full details and data files)

Version 1.0: 2023-04-19
Type: Initial release
Version 1.1: 2024-02-07
Changes: Data collection, Refinement description

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.